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Expressed Variant Reporting
Brandon Michael Blobner, Jenny Leopoldina Smith, and Ahmad Al Khleifat
2021-04-20
1 About The Test: Variant Detection from RNA-seq
snpReportR: A Method for RNAseq Variant Detection Reporting
| Information | Value |
|---|---|
| Name: | Jane Doe |
| DOB: | 01/01/1900 |
| Sex: | F |
| Sample Type: | RNA |
| Information | Value |
|---|---|
| Name: | Dr.X |
| Doctor identification number: | 12345 |
| Hospital: | NCI |
This document will help you to understand the more important findings from a gene variant screening. The common definitions of the type of genetic variants (mutations) are described in the figure and in the table in section Chromosome and Gene Vizualization of Mutations.
While a variant may have been detected, the associations with the variant are not perfectly causal and their complex interactions between biology and the environment.
2 About the Dataset
Table 1. Column names and Descriptions
In addition there are functional annotations for the variants per transcript from snpEFF. These include:
- “Annotation_Impact”
- “Feature_Type”
- “Transcript_BioType”
- “Rank”
- “HGVS.c”
- “HGVS.p”
- “cDNA.pos/cDNA.length”
- “CDS.pos/CDS.length”
- “AA.pos/AA.length”
- “Distance”
The top variants were ranked by the following attributes:
- FATHMM predicted pathogenicty or splice adjacent
- CHASMplus predicts driver mutations
- genes with larger number of SNVs prioritized
- high or moderate impact on the structure of the gene
- CADD Score/Polyphen Score (not done yet)
Interpretation of attributes
- “[FATHMM] weighted algorithm is capable of adjusting our conservation-based predictions to account for the tolerance of related sequences to mutations” (http://fathmm.biocompute.org.uk/inherited.html)
- “CHASMplus scores range from 0 to 1, with higher scores meaning more likely to be a cancer driver mutation.” (https://chasmplus.readthedocs.io/en/latest/)
- “VEST‐indel scores were assigned to categories of pathogenic (≥0.5) or benign (<0.5).” (https://doi.org/10.1002/humu.22911)
3 HumanMine Annotation for Further Results
## [1] "KRAS" "KEAP1" "PLK1" "FUS" "PDIA6"Expression of Genes with identified variants/SNVs in Normal Tissues.
4 Results Table
Included here are two tables for different gene types. Coding refers to genes that produce proteins, while non-coding refers to genes which do get utilized to produce proteins.
4.1 Coding Genes
4.2 Non-Coding Genes
5 Chromosome and Gene Vizualization of Mutations
| Type | Description |
|---|---|
| coding: | Mutation is within a coding region |
| 5prime_UTR: | Mutation is within 5’ untranslated region |
| 3prime_UTR: | Mutation is with 3’ untranslated region |
| introninc: | Mutation is with an intron region |
| splice: | Mutation is within proximity to a splice-site. |
| synonymous_variant: | Synonymous variant is a mutation in an exon that results in same amino acid (changed codon) |
| missense_variant: | Missense variant is a mutation in an exon that results in a different amino acid (changed codon) |
| start/stop: | Mutation is within a start/stop codon. |
Figure 1. Percentage of different types of mutations identified.
# Add Lollipop plot - interactive6 Expression of Genes with Mutations
6.1 boxplots/violin plots
| Symbol | GeneID | DRR132310_H1299_1.0.bam | DRR132321_H1299_0.1.bam | DRR132333_H1299_.01.bam | DRR131576_A549_1.0.bam | DRR131588_A549_0.1.bam | DRR131599_A549_.01.bam |
|---|---|---|---|---|---|---|---|
| TACC2 | 10579 | 3.49 | 4.54 | 4.63 | 5.25 | 3.67 | 4.94 |
| KRAS | 3845 | 5.73 | 6.20 | 5.57 | 5.94 | 4.44 | 5.73 |
| PLK1 | 5347 | 8.96 | 8.87 | 9.14 | 8.85 | 8.64 | 8.91 |
| FUS | 2521 | 8.08 | 8.07 | 7.73 | 7.42 | 7.68 | 7.16 |
| SLC25A11 | 8402 | 6.14 | 6.52 | 6.28 | 7.93 | 8.11 | 8.01 |
| KEAP1 | 9817 | 7.07 | 7.40 | 6.81 | 6.85 | 6.62 | 7.54 |
| GPATCH1 | 55094 | 5.37 | 5.33 | 5.28 | 5.45 | 0.62 | 4.67 |
| PDIA6 | 10130 | 8.11 | 7.93 | 8.24 | 9.17 | 8.74 | 9.00 |
| TCEA2 | 6919 | 2.76 | 1.21 | 3.22 | 3.67 | 0.62 | 2.76 |
| CD2AP | 23607 | 6.53 | 6.23 | 6.01 | 5.62 | 4.67 | 5.20 |
| FUCA2 | 2519 | 8.50 | 8.50 | 8.34 | 7.64 | 8.37 | 8.12 |
| FGL1 | 2267 | 0.62 | 0.62 | 0.62 | 7.15 | 7.12 | 6.66 |
Expression of the genes with pathogenic variants identified.
6.2 DE genes by condition
7 Sommelier results: Haplyotype/PCA
# add results here8 What Does This Result Mean for you? And What’s Next?
Genetic tests sometimes reveal information that could be relevant to your family such as a health risk that might run in the family, or that family relationships are different from what you expected.
Can you please add this message in the next steps section, if the report show an association with a gene. Please contact your doctor and a genetic counselor. A genetic counselor can help you understand:
- how your family members may be affected if the test shows a serious health condition runs in your family.
- the risk of you and your partner passing on a health condition to your children your options if you have a child with an inherited health condition and you do not want your next child to inherit it
- genetic counselor can also direct you to relevant patient support group
# Need diagram here9 More information
9.1 Recent Publications
9.2 Potential Drug Targets
Can search for additional drugs that may target the mutant genes online using Drug Targetor and at Drug Gene Interaction Database
# add drug target data information9.3 Potential Clinical Trials
# search API at https://clinicaltrials.gov/api/9.4 Web resources
# Add QR code where does it go?10 Consent for Analysis
This should simply be a copy of the consent form the patient has already signed. Also, interactive shiny widgets make this less portable.
11 Quality Control
11.1 Embed the IGV output from CTAT Mutation pipeline.
# embed file here11.2 Sequencing Depth and QC
# include Deeptools plots for coverage, average
# base quality scores, alignment quality scores,
# etc.12 References:
12.1 Citations
Smith RN, et al. InterMine: a flexible data warehouse system for the integration and analysis of heterogeneous biological data. Bioinformatics. 2012 Dec 1;28(23):3163-5.
12.2 Genome References and Software
12.3 Additional information about the pipelines used, check out the github repositories listed below:
## TxDb object:
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